OpenRaiser/Intern-Atlas huggingface dataset:
Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening
Venue: arXiv cs.LG 2024
Year: 2024

Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking models increases as the size of the compound library increases. Recently, deep learning algorithms can provide data-driven research and development models to increase the speed of the docking process. Unfortunately, few models can achieve superior screening performance compared to that of traditional models. Therefore, a novel deep learning-based docking approach named Dockformer is introduced in this study. Dockformer leverages multimodal information to capture the geometric topology and structural knowledge of molecules and can directly generate binding conformations with the corresponding confidence measures in an end-to-end manner. The experimental results show that Dockformer achieves success rates of 90.53% and 82.71% on the PDBbind core set and PoseBusters benchmarks, respectively, and more than a 100-fold increase in the inference process speed, outperforming almost all state-of-the-art docking methods. In addition, the ability of Dockformer to identify the main protease inhibitors of coronaviruses is demonstrated in a real-world virtual screening scenario. Considering its high docking accuracy and screening efficiency, Dockformer can be regarded as a powerful and robust tool in the field of drug design.
DP and QP Based Decision-making and Planning for Autonomous Vehicle
Venue: arXiv cs.RO 2024
Year: 2024

Autonomous driving technology is rapidly evolving and becoming a pivotal element of modern automation systems. Effective decision-making and planning are essential to ensuring autonomous vehicles operate safely and efficiently in complex environments. This paper introduces a decision-making and planning framework for autonomous vehicles, leveraging dynamic programming (DP) for global path planning and quadratic programming (QP) for local trajectory optimization. The proposed approach utilizes S-T graphs to achieve both dynamic and static obstacle avoidance. A comprehensive vehicle dynamics model supports the control system, enabling precise path tracking and obstacle handling. Simulation studies are conducted to evaluate the system's performance in a variety of scenarios, including global path planning, static obstacle avoidance, and dynamic obstacle avoidance involving pedestrian interactions. The results confirm the effectiveness and robustness of the proposed decision-making and planning algorithms in navigating complex environments, demonstrating the feasibility of this approach for autonomous driving applications.
Boosting the Targeted Transferability of Adversarial Examples via Salient Region & Weighted Feature Drop
Venue: arXiv cs.IR 2024
Year: 2024

Deep neural networks can be vulnerable to adversarially crafted examples, presenting significant risks to practical applications. A prevalent approach for adversarial attacks relies on the transferability of adversarial examples, which are generated from a substitute model and leveraged to attack unknown black-box models. Despite various proposals aimed at improving transferability, the success of these attacks in targeted black-box scenarios is often hindered by the tendency for adversarial examples to overfit to the surrogate models. In this paper, we introduce a novel framework based on Salient region & Weighted Feature Drop (SWFD) designed to enhance the targeted transferability of adversarial examples. Drawing from the observation that examples with higher transferability exhibit smoother distributions in the deep-layer outputs, we propose the weighted feature drop mechanism to modulate activation values according to weights scaled by norm distribution, effectively addressing the overfitting issue when generating adversarial examples. Additionally, by leveraging salient region within the image to construct auxiliary images, our method enables the adversarial example's features to be transferred to the target category in a model-agnostic manner, thereby enhancing the transferability. Comprehensive experiments confirm that our approach outperforms state-of-the-art methods across diverse configurations. On average, the proposed SWFD raises the attack success rate for normally trained models and robust models by 16.31% and 7.06% respectively.
White-Box Diffusion Transformer for single-cell RNA-seq generation
Venue: arXiv cs.LG 2024
Year: 2024

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer
Electrooculography Dataset for Objective Spatial Navigation Assessment in Healthy Participants
Venue: arXiv cs.HC 2024
Year: 2024

In the quest for understanding human executive function, eye movements represent a unique insight into how we process and comprehend our environment. Eye movements reveal patterns in how we focus, navigate, and make decisions across various contexts. The proposed dataset includes electrooculography (EOG) signals from 27 healthy subjects, capturing both vertical and horizontal eye movements. The recorded signals were obtained during the video-watching stage of the Leiden Navigation Test, designed to assess spatial navigation abilities. In addition to other data, the dataset includes scores from the Mini- Mental State Examination and the Wayfinding Questionnaire. The dataset comprises carefully curated components, including relevant information, the Mini-Mental State Examination scores, and the Wayfinding Questionnaire scores, encompassing navigation, orientation, distance estimation, spatial anxiety, as well as raw and processed EOG signals. These assessments contribute more information about the participants' cognitive function and navigational abilities. This dataset can be valuable for researchers investigating spatial navigation abilities through EOG signal analysis.
Large Language Model in Medical Informatics: Direct Classification and Enhanced Text Representations for Automatic ICD Coding
Venue: arXiv cs.LG 2024
Year: 2024

Addressing the complexity of accurately classifying International Classification of Diseases (ICD) codes from medical discharge summaries is challenging due to the intricate nature of medical documentation. This paper explores the use of Large Language Models (LLM), specifically the LLAMA architecture, to enhance ICD code classification through two methodologies: direct application as a classifier and as a generator of enriched text representations within a Multi-Filter Residual Convolutional Neural Network (MultiResCNN) framework. We evaluate these methods by comparing them against state-of-the-art approaches, revealing LLAMA's potential to significantly improve classification outcomes by providing deep contextual insights into medical texts.
Scientific machine learning in ecological systems: A study on the predator-prey dynamics
Venue: arXiv cs.LG 2024
Year: 2024

In this study, we apply two pillars of Scientific Machine Learning: Neural Ordinary Differential Equations (Neural ODEs) and Universal Differential Equations (UDEs) to the Lotka Volterra Predator Prey Model, a fundamental ecological model describing the dynamic interactions between predator and prey populations. The Lotka-Volterra model is critical for understanding ecological dynamics, population control, and species interactions, as it is represented by a system of differential equations. In this work, we aim to uncover the underlying differential equations without prior knowledge of the system, relying solely on training data and neural networks. Using robust modeling in the Julia programming language, we demonstrate that both Neural ODEs and UDEs can be effectively utilized for prediction and forecasting of the Lotka-Volterra system. More importantly, we introduce the forecasting breakdown point: the time at which forecasting fails for both Neural ODEs and UDEs. We observe how UDEs outperform Neural ODEs by effectively recovering the underlying dynamics and achieving accurate forecasting with significantly less training data. Additionally, we introduce Gaussian noise of varying magnitudes (from mild to high) to simulate real-world data perturbations and show that UDEs exhibit superior robustness, effectively recovering the underlying dynamics even in the presence of noisy data, while Neural ODEs struggle with high levels of noise. Through extensive hyperparameter optimization, we offer insights into neural network architectures, activation functions, and optimizers that yield the best results. This study opens the door to applying Scientific Machine Learning frameworks for forecasting tasks across a wide range of ecological and scientific domains.
Multi-Modal interpretable automatic video captioning
Venue: arXiv cs.CV 2024
Year: 2024

Video captioning aims to describe video contents using natural language format that involves understanding and interpreting scenes, actions and events that occurs simultaneously on the view. Current approaches have mainly concentrated on visual cues, often neglecting the rich information available from other important modality of audio information, including their inter-dependencies. In this work, we introduce a novel video captioning method trained with multi-modal contrastive loss that emphasizes both multi-modal integration and interpretability. Our approach is designed to capture the dependency between these modalities, resulting in more accurate, thus pertinent captions. Furthermore, we highlight the importance of interpretability, employing multiple attention mechanisms that provide explanation into the model's decision-making process. Our experimental results demonstrate that our proposed method performs favorably against the state-of the-art models on commonly used benchmark datasets of MSR-VTT and VATEX.
DynaShard: Secure and Adaptive Blockchain Sharding Protocol with Hybrid Consensus and Dynamic Shard Management
Venue: arXiv cs.DC 2024
Year: 2024

Blockchain sharding has emerged as a promising solution to the scalability challenges in traditional blockchain systems by partitioning the network into smaller, manageable subsets called shards. Despite its potential, existing sharding solutions face significant limitations in handling dynamic workloads, ensuring secure cross-shard transactions, and maintaining system integrity. To address these gaps, we propose DynaShard, a dynamic and secure cross-shard transaction processing mechanism designed to enhance blockchain sharding efficiency and security. DynaShard combines adaptive shard management, a hybrid consensus approach, plus an efficient state synchronization and dispute resolution protocol. Our performance evaluation, conducted using a robust experimental setup with real-world network conditions and transaction workloads, demonstrates DynaShard's superior throughput, reduced latency, and improved shard utilization compared to the FTBS method. Specifically, DynaShard achieves up to a 42.6% reduction in latency and a 78.77% improvement in shard utilization under high transaction volumes and varying cross-shard transaction ratios. These results highlight DynaShard's ability to outperform state-of-the-art sharding methods, ensuring scalable and resilient blockchain systems. We believe that DynaShard's innovative approach will significantly impact future developments in blockchain technology, paving the way for more efficient and secure distributed systems.
Which PPML Would a User Choose? A Structured Decision Support Framework for Developers to Rank PPML Techniques Based on User Acceptance Criteria
Venue: arXiv cs.AI 2024
Year: 2024

Using Privacy-Enhancing Technologies (PETs) for machine learning often influences the characteristics of a machine learning approach, e.g., the needed computational power, timing of the answers or how the data can be utilized. When designing a new service, the developer faces the problem that some decisions require a trade-off. For example, the use of a PET may cause a delay in the responses or adding noise to the data to improve the users' privacy might have a negative impact on the accuracy of the machine learning approach. As of now, there is no structured way how the users' perception of a machine learning based service can contribute to the selection of Privacy Preserving Machine Learning (PPML) methods. This is especially a challenge since one cannot assume that users have a deep technical understanding of these technologies. Therefore, they can only be asked about certain attributes that they can perceive when using the service and not directly which PPML they prefer. This study introduces a decision support framework with the aim of supporting the selection of PPML technologies based on user preferences. Based on prior work analysing User Acceptance Criteria (UAC), we translate these criteria into differentiating characteristics for various PPML techniques. As a final result, we achieve a technology ranking based on the User Acceptance Criteria while providing technology insights for the developers. We demonstrate its application using the use case of classifying privacy-relevant information. Our contribution consists of the decision support framework which consists of a process to connect PPML technologies with UAC, a process for evaluating the characteristics that separate PPML techniques, and a ranking method to evaluate the best PPML technique for the use case.
Estimating Causal Effects in Partially Directed Parametric Causal Factor Graphs
Venue: arXiv cs.AI 2024
Year: 2024

Lifting uses a representative of indistinguishable individuals to exploit symmetries in probabilistic relational models, denoted as parametric factor graphs, to speed up inference while maintaining exact answers. In this paper, we show how lifting can be applied to causal inference in partially directed graphs, i.e., graphs that contain both directed and undirected edges to represent causal relationships between random variables. We present partially directed parametric causal factor graphs (PPCFGs) as a generalisation of previously introduced parametric causal factor graphs, which require a fully directed graph. We further show how causal inference can be performed on a lifted level in PPCFGs, thereby extending the applicability of lifted causal inference to a broader range of models requiring less prior knowledge about causal relationships.
Leveraging LSTM for Predictive Modeling of Satellite Clock Bias
Venue: arXiv cs.LG 2024
Year: 2024

Satellite clock bias prediction plays a crucial role in enhancing the accuracy of satellite navigation systems. In this paper, we propose an approach utilizing Long Short-Term Memory (LSTM) networks to predict satellite clock bias. We gather data from the PRN 8 satellite of the Galileo and preprocess it to obtain a single difference sequence, crucial for normalizing the data. Normalization allows resampling of the data, ensuring that the predictions are equidistant and complete. Our methodology involves training the LSTM model on varying lengths of datasets, ranging from 7 days to 31 days. We employ a training set consisting of two days' worth of data in each case. Our LSTM model exhibits exceptional accuracy, with a Root Mean Square Error (RMSE) of 2.11 $\times$ 10$^{-11}$. Notably, our approach outperforms traditional methods used for similar time-series forecasting projects, being 170 times more accurate than RNN, 2.3 $\times$ 10$^7$ times more accurate than MLP, and 1.9 $\times$ 10$^4$ times more accurate than ARIMA. This study holds significant potential in enhancing the accuracy and efficiency of low-power receivers used in various devices, particularly those requiring power conservation. By providing more accurate predictions of satellite clock bias, the findings of this research can be integrated into the algorithms of such devices, enabling them to function with heightened precision while conserving power. Improved accuracy in clock bias predictions ensures that low-power receivers can maintain optimal performance levels, thereby enhancing the overall reliability and effectiveness of satellite navigation systems. Consequently, this advancement holds promise for a wide range of applications, including remote areas, IoT devices, wearable technology, and other devices where power efficiency and navigation accuracy are paramount.
Evaluating the Accuracy of Chatbots in Financial Literature
Venue: arXiv cs.AI 2024
Year: 2024

We evaluate the reliability of two chatbots, ChatGPT (4o and o1-preview versions), and Gemini Advanced, in providing references on financial literature and employing novel methodologies. Alongside the conventional binary approach commonly used in the literature, we developed a nonbinary approach and a recency measure to assess how hallucination rates vary with how recent a topic is. After analyzing 150 citations, ChatGPT-4o had a hallucination rate of 20.0% (95% CI, 13.6%-26.4%), while the o1-preview had a hallucination rate of 21.3% (95% CI, 14.8%-27.9%). In contrast, Gemini Advanced exhibited higher hallucination rates: 76.7% (95% CI, 69.9%-83.4%). While hallucination rates increased for more recent topics, this trend was not statistically significant for Gemini Advanced. These findings emphasize the importance of verifying chatbot-provided references, particularly in rapidly evolving fields.
Towards Characterizing Cyber Networks with Large Language Models
Venue: arXiv cs.AI 2024
Year: 2024

Threat hunting analyzes large, noisy, high-dimensional data to find sparse adversarial behavior. We believe adversarial activities, however they are disguised, are extremely difficult to completely obscure in high dimensional space. In this paper, we employ these latent features of cyber data to find anomalies via a prototype tool called Cyber Log Embeddings Model (CLEM). CLEM was trained on Zeek network traffic logs from both a real-world production network and an from Internet of Things (IoT) cybersecurity testbed. The model is deliberately overtrained on a sliding window of data to characterize each window closely. We use the Adjusted Rand Index (ARI) to comparing the k-means clustering of CLEM output to expert labeling of the embeddings. Our approach demonstrates that there is promise in using natural language modeling to understand cyber data.
Impact of LLM-based Review Comment Generation in Practice: A Mixed Open-/Closed-source User Study
Venue: arXiv cs.SE 2024
Year: 2024

We conduct a large-scale empirical user study in a live setup to evaluate the acceptance of LLM-generated comments and their impact on the review process. This user study was performed in two organizations, Mozilla (which has its codebase available as open source) and Ubisoft (fully closed-source). Inside their usual review environment, participants were given access to RevMate, an LLM-based assistive tool suggesting generated review comments using an off-the-shelf LLM with Retrieval Augmented Generation to provide extra code and review context, combined with LLM-as-a-Judge, to auto-evaluate the generated comments and discard irrelevant cases. Based on more than 587 patch reviews provided by RevMate, we observed that 8.1% and 7.2%, respectively, of LLM-generated comments were accepted by reviewers in each organization, while 14.6% and 20.5% other comments were still marked as valuable as review or development tips. Refactoring-related comments are more likely to be accepted than Functional comments (18.2% and 18.6% compared to 4.8% and 5.2%). The extra time spent by reviewers to inspect generated comments or edit accepted ones (36/119), yielding an overall median of 43s per patch, is reasonable. The accepted generated comments are as likely to yield future revisions of the revised patch as human-written comments (74% vs 73% at chunk-level).
Topological Characterization of Stabilizing Consensus
Venue: arXiv cs.DC 2024
Year: 2024

We provide a complete characterization of the solvability/impossibility of deterministic stabilizing consensus in any computing model with benign process and communication faults using point-set topology. Relying on the topologies for infinite executions introduced by Nowak, Schmid and Winkler (JACM, 2024) for terminating consensus, we prove that semi-open decision sets and semi-continuous decision functions as introduced by Levin (AMM, 1963) are the appropriate means for this characterization: Unlike the decision functions for terminating consensus, which are continuous, semi-continuous functions do not require the inverse image of an open set to be open and hence allow to map a connected space to a disconnected one. We also show that multi-valued stabilizing consensus with weak and strong validity are equivalent, as is the case for terminating consensus. By applying our results to (variants of) all the known possibilities/impossibilities for stabilizing consensus, we easily provide a topological explanation of these results.
Fast and Robust Contextual Node Representation Learning over Dynamic Graphs
Venue: arXiv cs.LG 2024
Year: 2024

Real-world graphs grow rapidly with edge and vertex insertions over time, motivating the problem of efficiently maintaining robust node representation over evolving graphs. Recent efficient GNNs are designed to decouple recursive message passing from the learning process, and favor Personalized PageRank (PPR) as the underlying feature propagation mechanism. However, most PPR-based GNNs are designed for static graphs, and efficient PPR maintenance remains as an open problem. Further, there is surprisingly little theoretical justification for the choice of PPR, despite its impressive empirical performance. In this paper, we are inspired by the recent PPR formulation as an explicit $\ell_1$-regularized optimization problem and propose a unified dynamic graph learning framework based on sparse node-wise attention. We also present a set of desired properties to justify the choice of PPR in STOA GNNs, and serves as the guideline for future node attention designs. Meanwhile, we take advantage of the PPR-equivalent optimization formulation and employ the proximal gradient method (ISTA) to improve the efficiency of PPR-based GNNs upto 6 times. Finally, we instantiate a simple-yet-effective model (\textsc{GoPPE}) with robust positional encodings by maximizing PPR previously used as attention. The model performs comparably to or better than the STOA baselines and greatly outperforms when the initial node attributes are noisy during graph evolution, demonstrating the effectiveness and robustness of \textsc{GoPPE}.